Data Quality Assessment Report
massqc from tidymass by Xiaotao Shen
2022-09-20
PARAMETERS
Table 1: Parameter setting
| pacakge_name | function_name | parameter | time |
|---|---|---|---|
| massprocesser | process_data | path:01.mzxml/NEG/ | 2022-09-20 15:19:27 |
| massprocesser | process_data | polarity:negative | 2022-09-20 15:19:27 |
| massprocesser | process_data | ppm:10 | 2022-09-20 15:19:27 |
| massprocesser | process_data | peakwidth:10,60 | 2022-09-20 15:19:27 |
| massprocesser | process_data | snthresh:5 | 2022-09-20 15:19:27 |
| massprocesser | process_data | prefilter:3,500 | 2022-09-20 15:19:27 |
| massprocesser | process_data | fitgauss:FALSE | 2022-09-20 15:19:27 |
| massprocesser | process_data | integrate:2 | 2022-09-20 15:19:27 |
| massprocesser | process_data | mzdiff:0.01 | 2022-09-20 15:19:27 |
| massprocesser | process_data | noise:500 | 2022-09-20 15:19:27 |
| massprocesser | process_data | threads:100 | 2022-09-20 15:19:27 |
| massprocesser | process_data | binSize:0.025 | 2022-09-20 15:19:27 |
| massprocesser | process_data | bw:5 | 2022-09-20 15:19:27 |
| massprocesser | process_data | output_tic:TRUE | 2022-09-20 15:19:27 |
| massprocesser | process_data | output_bpc:TRUE | 2022-09-20 15:19:27 |
| massprocesser | process_data | output_rt_correction_plot:TRUE | 2022-09-20 15:19:27 |
| massprocesser | process_data | min_fraction:0.2 | 2022-09-20 15:19:27 |
| massprocesser | process_data | fill_peaks:FALSE | 2022-09-20 15:19:27 |
| massdataset | create_mass_dataset() | no:no | 2022-09-20 15:21:32 |
| massdataset | mutate() | parameter_1:batch=rep(c(“1”, “2”), c(7, 23 - 6)) | 2022-09-20 15:41:14 |
SAMPLE INFORMATION
#> --------------------
#> massdataset version: 1.0.5
#> --------------------
#> 1.expression_data:[ 12316 x 24 data.frame]
#> 2.sample_info:[ 24 x 5 data.frame]
#> 3.variable_info:[ 12316 x 3 data.frame]
#> 4.sample_info_note:[ 5 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> --------------------
#> Processing information (extract_process_info())
#> create_mass_dataset ----------
#> Package Function.used Time
#> 1 massdataset create_mass_dataset() 2022-09-20 15:21:32
#> process_data ----------
#> Package Function.used Time
#> 1 massprocesser process_data 2022-09-20 15:19:27
#> mutate ----------
#> Package Function.used Time
#> 1 massdataset mutate() 2022-09-20 15:41:14
Figure 1: Peak intensity profile.
MISSING VALUES
MISSING VALUES IN DATASET
Black is MV.
Figure 2: Missing values in dataset
MISSING VALUES IN VARIABLES
Figure 3: Missing values in variables
MISSING VALUES IN SAMPLES
Figure 4: Missing values in samples
RSD DISTRIBUTATION
Figure 5: RSD distributation
INTENSITY FOR ALL THE VARIABLES
Figure 6: Intensity for all the variables
SAMPLE CORRELATION
Figure 7: Sample correlation
PCA score plot
